CRISPR and Genetic Engineering

The paper introduces EasyGuide CRISPR, a CRISPR toolkit for engineering E. coli strains to grow on sucrose, and demonstrates its application in adaptive evolution experiments.

The paper develops an all-RNA prime editing system achieving over 95% editing efficiency in human iPSCs with minimal off-target effects.

This paper develops a stochastic model to simulate homing gene drive frequency dynamics and identifies conditions leading to intermediate outcomes, providing a web tool for safer gene drive design.

This paper describes a CRISPR-Cas13b-based method to edit the T4 bacteriophage genome, enabling gene deletions, mutations, and fluorescent protein insertion for studying phage biology.

This study develops Cas9 and Un1Cas12f1 gene drives in HSV1 to assess gene drive efficacy and resistance, finding Un1Cas12f1 has higher conversion and lower resistance.

GO-CRISPR improves loss-of-function CRISPR screens by integrating guide-only controls and TRACS software, identifying novel pathways in tumor dormancy.

This study shows CRISPR-Cas13b effectively reduces DUX4 in FSHD but is limited by immune responses that decrease Cas13b levels over time.

This paper introduces XSTART, a PAM-independent base editing system for universal gene inactivation in bacteria, achieving near 100% efficiency but with off-target events.

The paper introduces PIPOline, a computational tool for designing plasmids for marker-free genome editing in budding yeast, and demonstrates its application for gene tagging and deletion.

The paper benchmarks multiple base editors and develops a model to predict editing efficiency, validating edits for disease-associated variants and identifying cancer-related SNVs.

KOnezumi-AID automates gRNA design for Target-AID-mediated gene knockouts, enabling efficient and safe multiplex knockout strategies in mouse and human genomes.

This study develops stabilized Cas-embedded base editors (sCE_CBEs) that enable efficient and accurate C-to-T editing with minimal off-target effects in hematopoietic stem and progenitor cells.

This paper introduces a high-accuracy CRISPR array assembly strategy that enables efficient assembly of multiple crRNAs in a single reaction, improving the practicality of multiplex CRISPR applications.

This study shows that gene editing of HSCs without ex vivo culture reduces genotoxicity while maintaining therapeutic efficacy for beta-hemoglobinopathy treatment.

This study tests mitochondrial adenine base editing in mouse tissues via AAV delivery, finding low and modestly increasing editing efficiency over time.

This study develops and validates an efficient method for in situ epitope tagging of rice genes using prime editing, demonstrating its utility for gene function studies and genetic improvement.

This paper develops a degron-modified Cas12a system to enable accurate single-cell detection of pre-crRNAs, enhancing Perturb-seq capabilities for multiplex guide expression.

The paper introduces a scalable method to upregulate plant gene expression using a genomic model and MPRA, identifying functional cis-regulatory elements without prior knowledge.

This study identifies SspA as a transcriptional regulator of CRISPR adaptation in E. coli using a CRISPRi-based screen and proposes a model of independent cellular control of adaptation and interference by SspA.

Crackling Cloud is a cloud-based tool for designing CRISPR-Cas9 guide RNAs, offering scalability and accessibility without requiring local high-performance computing resources.

This study applies CASAAV-HDR to model cardiomyopathies and perform functional genomics in mouse cardiomyocytes, showing its utility for disease modeling and enhancer analysis.

The paper shows that CRISPR-based methods for studying miRNA binding sites in isogenic cell lines are unreliable due to high variability between replicates.

This paper introduces RecombiCraft, a method for DNA library construction in E. coli using SLiCE and liquid culture, which minimizes sequence bias and reduces costs.

This study shows that the Cas10 nuclease activity in type III-A CRISPR-Cas systems relieves host dormancy to enable spacer acquisition and retention, enhancing broad-spectrum immunity.

The paper develops and validates fluorescence-based CRISPRi tools for gene repression and live single-cell imaging in mycobacteria.

The paper describes a cost-effective method for mouse genome editing using i-GONAD and CRISPR/Cas9, achieving IL10 gene knockout in 30.8% of pups.

This study shows that type VI-B CRISPR-Cas systems with RT-Cas1 fusion proteins can acquire spacers from RNA, functioning independently of other systems.

This paper adapts the CRISPR-Cas13d system for targeted gene expression knockdown in chick embryos, demonstrating effective PAX7 knockdown comparable to morpholino.

The paper presents a genome-scale CRISPRi perturbation map in human pluripotent stem cells using single-cell RNA sequencing to study trans gene regulation across diverse genetic backgrounds.

SPLICER improves exon skipping by editing both splice acceptor and donor sites, reducing aberrant splicing and enabling therapeutic applications in Alzheimer's disease.